In [1]:
suppressMessages(library(ArchR))
ss <- function(x, pattern, slot = 1, ...) { sapply(strsplit(x = x, split = pattern, ...), '[', slot) }
options(stringsAsFactors = F)
options(repr.plot.width=11, repr.plot.height=8.5)
Warning message: “package ‘gtable’ was built under R version 4.1.3” Warning message: “package ‘magrittr’ was built under R version 4.1.3” Warning message: “package ‘plyr’ was built under R version 4.1.3” Warning message: “package ‘stringr’ was built under R version 4.1.3” Warning message: “package ‘data.table’ was built under R version 4.1.3” Warning message: “package ‘Matrix’ was built under R version 4.1.3” Warning message: “package ‘Rcpp’ was built under R version 4.1.3”
In [2]:
##################################
### set Arrow File parameters ####
addArchRThreads(threads = 5)
##################################
### load rheMac10 ArchR genome ###
GENOMEDIR='/home/bnphan/resources/genomes/rn7'
load(file.path(GENOMEDIR,'rn7_liftoff_mm10NcbiRefSeq_ArchR_annotations.rda'))
Setting default number of Parallel threads to 5.
In [3]:
PROJDIR='/projects/pfenninggroup/singleCell/Pierce_transgen_rat_multiome/data/tidy_data/ArchRProjects'
ARCHDIR=file.path(PROJDIR,'Rat_Transgen_NAc_scATAC')
proj = loadArchRProject(ARCHDIR)
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
Make plots¶
In [4]:
proj
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
class: ArchRProject outputDirectory: /projects/pfenninggroup/singleCell/Pierce_transgen_rat_multiome/data/tidy_data/ArchRProjects/Rat_Transgen_NAc_scATAC samples(5): 1S 2M 3C 4S 5M sampleColData names(1): ArrowFiles cellColData names(18): Sample TSSEnrichment ... ClustersI200_ATAC ClustersH200_ATAC numberOfCells(1): 38784 medianTSS(1): 4.814 medianFrags(1): 11511.5
In [5]:
# plot the confusion matrix of cell types by subjects
cM <- confusionMatrix(proj$Sample, proj$ClustersH200_ATAC)
cM <- cM / Matrix::colSums(cM)
p <- pheatmap::pheatmap(
mat = as.matrix(cM),
color = paletteContinuous("whiteBlue"),
border_color = "black")
p
In [6]:
## make UMAP plots
p1 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "ClustersH200_ATAC", embedding = "UMAPH200_ATAC", imputeWeights = NULL)
p3 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "Sire", embedding = "UMAPH200_ATAC", imputeWeights = NULL)
ggAlignPlots(p1, p3, type = "h")
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-26140224f1313-Date-2022-12-05_Time-12-47-24.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-26140224f1313-Date-2022-12-05_Time-12-47-24.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-261401bfe833d-Date-2022-12-05_Time-12-47-27.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-261401bfe833d-Date-2022-12-05_Time-12-47-27.log
In [7]:
p1 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "ClustersH200_ATAC", embedding = "UMAPH200_ATAC", imputeWeights = NULL)
p3 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "Sample", embedding = "UMAPH200_ATAC", imputeWeights = NULL)
ggAlignPlots(p1, p3, type = "h")
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-26140542bf0d1-Date-2022-12-05_Time-12-47-34.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-26140542bf0d1-Date-2022-12-05_Time-12-47-34.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-26140505d49ca-Date-2022-12-05_Time-12-47-34.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-26140505d49ca-Date-2022-12-05_Time-12-47-34.log
In [8]:
## make UMAP plots of
p1 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "ClustersH200_ATAC", embedding = "UMAPH200_ATAC", imputeWeights = NULL)
p2 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "DoubletEnrichment", embedding = "UMAPH200_ATAC", imputeWeights = NULL)
ggAlignPlots(p1, p2, type = "h")
proj$logNFrags = log10(proj$nFrags)
p3 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "logNFrags", embedding = "UMAPH200_ATAC", imputeWeights = NULL)
ggAlignPlots(p1, p3, type = "h")
p4 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "TSSEnrichment", embedding = "UMAPH200_ATAC", imputeWeights = NULL)
ggAlignPlots(p1, p4, type = "h")
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-261403fa7ff9e-Date-2022-12-05_Time-12-47-39.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-261403fa7ff9e-Date-2022-12-05_Time-12-47-39.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-261405d685375-Date-2022-12-05_Time-12-47-40.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 Warning message: “package ‘hexbin’ was built under R version 4.1.3” ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-261405d685375-Date-2022-12-05_Time-12-47-40.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-261404a593298-Date-2022-12-05_Time-12-47-44.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-261404a593298-Date-2022-12-05_Time-12-47-44.log
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-261402331d5dc-Date-2022-12-05_Time-12-47-49.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-261402331d5dc-Date-2022-12-05_Time-12-47-49.log
In [9]:
## Neuron vs. Glia markers
markerGenes1 <- c('Rbfox3', # Neuron
'Lhx6', #Interneuron
'Aqp4', # Astrocyte
'Cx3cr1', # Microglia
'Pdgfra', #OPC
'Mog' # Oligo
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200_ATAC", imputeWeights = NULL)
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-2614069e50858-Date-2022-12-05_Time-12-47-54.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-12-05 12:47:54 : Plotting Embedding 1 2 3 4 5 6 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-2614069e50858-Date-2022-12-05_Time-12-47-54.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
In [10]:
# Broad MSN marker, mouse 2010900C02Rik == human KIAA1211L
# MSN markers, Ppp1r1b = DARPP-32, Bcl11b=Ctip2
markMSN3 = c('Ppp1r1b','Bcl11b','Foxp1','Six3','Slc17a7' )
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markMSN3, embedding = "UMAPH200_ATAC", imputeWeights = NULL)
p3 <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p3))
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-2614022af9778-Date-2022-12-05_Time-12-48-32.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-12-05 12:48:32 : Plotting Embedding 1 2 3 4 5 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-2614022af9778-Date-2022-12-05_Time-12-48-32.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
In [11]:
markMSN1 = c('Drd1','Tac1','Foxp2','Slc17a7','Chrm4', 'Pdyn') # D1 markers
# D1 MSN
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markMSN1, embedding = "UMAPH200_ATAC", imputeWeights = NULL) #
p1 <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) +
theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p1))
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-261403cb5ea7-Date-2022-12-05_Time-12-49-01.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-12-05 12:49:01 : Plotting Embedding 1 2 3 4 5 6 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-261403cb5ea7-Date-2022-12-05_Time-12-49-01.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
In [12]:
markMSN2 = c('Drd2','Adora2a','Penk', 'Grik3', 'Sp9', 'Gpr52')# D2 markers
# D2 MSN
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markMSN2, embedding = "UMAPH200_ATAC", imputeWeights = NULL)
p2 <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p2))
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-261407a0f987b-Date-2022-12-05_Time-12-49-31.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-12-05 12:49:31 : Plotting Embedding 1 2 3 4 5 6 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-261407a0f987b-Date-2022-12-05_Time-12-49-31.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
In [13]:
## plot more interneuron markers
markerGenes1 <- c('Lhx6', "Pvalb",'Pthlh','Cck', 'Sst', 'Chat','Th', 'Vip') # Interneuron markers
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200_ATAC", imputeWeights = NULL)
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(nrow = 2),p))
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-261402eefc845-Date-2022-12-05_Time-12-50-01.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-12-05 12:50:01 : Plotting Embedding 1 2 3 4 5 6 7 8 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-261402eefc845-Date-2022-12-05_Time-12-50-01.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
In [14]:
## plot Excitatory neuron markers for major class and upper layers
markerGenes1 <- c(
'Rbfox3', 'Slc17a7', 'Gad1', # Main classes
'Cux2', 'Meis2', "Rorb", # L3/ L4 IT
"Alpl", 'Tbx15') # L4/5)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200_ATAC", imputeWeights = NULL)
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(nrow =2),p))
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-26140762ea605-Date-2022-12-05_Time-12-50-37.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-12-05 12:50:37 : Plotting Embedding 1 2 3 4 5 6 7 8 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-26140762ea605-Date-2022-12-05_Time-12-50-37.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
In [15]:
## plot Excitatory neuron markers for deeper layers
markerGenes1 <- c(
'Themis', # Car3 and L6 IT
'Pou3f1', 'Pcp4', 'Nr4a2', # L5
'Fezf2', 'Foxp2',# NP and L6, L5 ET
'Syt6', 'Itga8' #L6
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200_ATAC", imputeWeights = NULL)
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(nrow = 2),p))
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-261402213005b-Date-2022-12-05_Time-12-51-16.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-12-05 12:51:17 : Plotting Embedding 1 2 3 4 5 6 7 8 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-261402213005b-Date-2022-12-05_Time-12-51-16.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
In [16]:
## plot more cortical interneuron markers
markerGenes1 <- c('Lhx6', "Pvalb", 'TRPS1', 'Sst', # MGE markers
'Adarb2', 'Vip', 'Sncg', 'Lamp5') # CGE markers
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200_ATAC", imputeWeights = NULL)
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(nrow = 2),p))
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-261402d50eeb9-Date-2022-12-05_Time-12-51-57.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-12-05 12:51:58 : Plotting Embedding 1 2 3 4 5 6 7 8 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-261402d50eeb9-Date-2022-12-05_Time-12-51-57.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Relabel cluster and call peaks¶
In [17]:
############################################
# using marker gene scores, give cluster names
# NO EXC, replace w/ MSN
remapClust <- c(
'C1' ='Drop',
'C2' ='Neuron',
'C3' ='Neuron',
'C4' ='Neuron',
'C5' ='Neuron',
'C6' ='Neuron',
'C7' ='Neuron',
'C8' ='Neuron',
'C9' ='Neuron',
'C10'='Drop',
'C11'='Drop',
'C12'='Microglia',
'C13'='Oligo',
'C14'='Astro',
'C15'='OPC'
)
proj$Celltype1 <- mapLabels(proj$ClustersH200_ATAC, newLabels = remapClust,
oldLabels = names(remapClust))
table(proj$Celltype1)
Astro Drop Microglia Neuron Oligo OPC
1135 12523 1081 19856 2714 1475
In [18]:
## make UMAP plots
p1 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "Celltype1", embedding = "UMAPH200_ATAC", imputeWeights = NULL)
p1
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-261402141924e-Date-2022-12-05_Time-13-02-34.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-261402141924e-Date-2022-12-05_Time-13-02-34.log
In [19]:
idxSample <- BiocGenerics::which(proj$Celltype1 != 'Drop' )
cellsSample <- proj$cellNames[idxSample]
proj2 = proj[cellsSample,]
table(proj2$Celltype1)
Dropping ImputeWeights Since You Are Subsetting Cells! ImputeWeights is a cell-x-cell Matrix!
Astro Microglia Neuron Oligo OPC
1135 1081 19856 2714 1475
In [20]:
proj = saveArchRProject(ArchRProj = proj2, dropCells = TRUE)
Moving Arrow Files (1 of 5)
Moving Arrow Files (2 of 5)
Moving Arrow Files (3 of 5)
Moving Arrow Files (4 of 5)
Moving Arrow Files (5 of 5)
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
In [20]:
# drop the drop clusters, pull out the neuron cell types
ARCHDIR2=file.path(PROJDIR,'Rat_Transgen_NAc_scATAC_Neuron')
neuronType = c('Neuron')
idxSample <- BiocGenerics::which(proj$Celltype1 %in% neuronType )
table(proj$Celltype1[idxSample])
cellsSample <- proj$cellNames[idxSample]
proj2 = subsetArchRProject(
ArchRProj = proj, cells = cellsSample,
outputDirectory = ARCHDIR2, force = TRUE
)
proj = saveArchRProject(ArchRProj = proj)
Neuron 21510
Dropping ImputeWeights Since You Are Subsetting Cells! ImputeWeights is a cell-x-cell Matrix!
Copying ArchRProject to new outputDirectory : /projects/pfenninggroup/singleCell/Pierce_transgen_rat_multiome/data/tidy_data/ArchRProjects/Rat_Transgen_NAc_scATAC_Neuron
Copying Arrow Files...
Getting ImputeWeights
No imputeWeights found, returning NULL
Copying Other Files...
Copying Other Files (1 of 2): Embeddings
Copying Other Files (2 of 2): IterativeLSI200_ATAC
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
In [ ]:
# drop the drop clusters, pull out the glia cell types
ARCHDIR2=file.path(PROJDIR,'Rat_Transgen_NAc_scATAC_Glia')
idxSample <- BiocGenerics::which(proj$Celltype1 %ni% c(neuronType, 'Drop'))
table(proj$Celltype1[idxSample])
cellsSample <- proj$cellNames[idxSample]
proj2 = subsetArchRProject(
ArchRProj = proj,
cells = cellsSample,
outputDirectory = ARCHDIR2, force = TRUE
)
In [ ]:
In [ ]: